Software

The workstations in the molecular modeling laboratory located in the Laboratory Science Commons — 2335 have a variety of software packages installed for molecular modeling and computational chemistry applications. Some of this software is free or open source software that is installed for all users, and other software is commercial software that Tennessee Tech University has purchased for faculty, student or staff use. If you require the user of a software package that is not currently installed on these systems, please contact the administrator to inquire about installing it.

Most of the free and open source software packages can be installed on student-owned computers if you wish to use it at home or on your own computer. Please note that any software downloaded via the internet to your own computer is installed at your own risk. Commercial software available in the lab under a license purchased by Tennessee Tech University cannot be installed on student-owned computers due to our license agreement.

Some of the software packages included in this list are for various instruments in other labs operated by the Department of Chemistry. If this is the case, that is noted below.

Autodock Vina

Autodock Vina is an open-source molecular modeling program for performing molecular docking calculations of small molecules. Autodock Vina significantly improves the average accuracy of the binding mode predictions compared to Autodock 4.

  • Command: vina
  • Manual: HTML

Avogadro 2

Avogadro 2 is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

  • Command: avogadro2
  • Manual: HTML

BioPerl / BioPython

BioPerl and BioPython are sets of freely available tools for biological computation written as an add-on resource to the Perl and Python programming languages. This is a distributed collaborative effort to develop libraries and applications which address the needs of current and future work in bioinformatics.

Gaussian ’09

Gaussian ’09 provides state-of-the-art capabilities for electronic structure modeling and is used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian ’09 predicts the energies, molecular structures, vibrational frequencies and molecular propertiesManual: of molecules and reactions in a wide variety of chemical environments.

The Avogadro and MOE molecular modeling software packages provide a a visualization and graphical user interface to the Gaussian ’09 engine.

  • Command: g09
  • Manual: PDF
  • Website: HTML (the newest version is Gaussian ’16, but many commands are still applicable to Gaussian ’09)

Gnu Image Manipulation Program (GIMP)

GIMP is an open-source, cross-platform image editor with basic image editing capabilities. One an think of this as a “free version” of Adobe Photoshop.

  • Command: gimp
  • Manual: HTML

GnuPlot

GnuPlot is a portable command-line driven graphing utility for Linux, Windows, and OS X. The source code is copyrighted but freely distributed (i.e., you don’t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.

  • Command: gnuplot
  • Manual: PDF
  • Scripts: HTML

GROMACS

GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

  • Command: There are multiple executables installed in /usr/bin for all users. Read the manual.
  • Manual: HTML

Maestro 10

Maestro is a powerful, all-purpose molecular modeling environment. It provides a unified interface for all Schrodinger software. It has rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers. The free academic version of this software is currently available.

  • Command: maestro
  • Manual: HTML

MOE 2022

MOE 2022 from Chemical Computing, Ltd., is available for the molecular modeling of large, macromolecular systems such as proteins and nucleic acids. It also interfaces with Gaussian 09 for quantum chemistry calculations of small molecule ligands and NAMD for molecular dynamics.

  • Command: moe
  • Manual: HTML (accessible on local systems only)

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD (see below) for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

ORCA

ORCA is an ab initio quantum chemistry program that contains modern electronic structure methods, such as density functional theory, many-body perturbation, coupled cluster, multireference methods and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes and their spectroscopic properties.

  • Command: orca
  • Manual: HTML

R

R is a free software environment for statistical computing and graphcis.

  • Command: R
  • Manual: HTML

Rosetta

The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It can be used for de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

UCSF Chimera X

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera X also includes an interface to Google Colab for running Alphafold2 protein folding simulations.

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

  • Command: vmd
  • Manual: HTML